@article{TEXTUAL,
      recid = {10454},
      author = {Altermann, Susanne and Leavitt, Steven D. and Goward,  Trevor and Nelsen, Matthew P. and Lumbsch, H. Thorsten},
      title = {How Do You Solve a Problem like  &amp;lt;i&amp;gt;Letharia&amp;lt;/i&amp;gt;? A New Look at Cryptic Species  in Lichen-Forming Fungi Using Bayesian Clustering and SNPs  from Multilocus Sequence Data},
      journal = {PLOS ONE},
      address = {2014-05-15},
      number = {TEXTUAL},
      abstract = {&lt;p&gt;The inclusion of molecular data is increasingly an  integral part of studies assessing species boundaries.  Analyses based on predefined groups may obscure patterns of  differentiation, and population assignment tests provide an  alternative for identifying population structure and  barriers to gene flow. In this study, we apply population  assignment tests implemented in the programs STRUCTURE and  BAPS to single nucleotide polymorphisms from DNA sequence  data generated for three previous studies of the lichenized  fungal genus &lt;em&gt;Letharia&lt;/em&gt;. Previous molecular work  employing a gene genealogical approach circumscribed six  species-level lineages within the genus, four putative  lineages within the nominal taxon &lt;em&gt;L. columbiana&lt;/em&gt;  (Nutt.) J.W. Thomson and two sorediate lineages. We show  that Bayesian clustering implemented in the program  STRUCTURE was generally able to recover the same six  putative &lt;em&gt;Letharia&lt;/em&gt; lineages. Population assignments  were largely consistent across a range of scenarios,  including: extensive amounts of missing data, the exclusion  of SNPs from variable markers, and inferences based on SNPs  from as few as three gene regions. While our study provided  additional evidence corroborating the six candidate  &lt;em&gt;Letharia&lt;/em&gt; species, the equivalence of these genetic  clusters with species-level lineages is uncertain due, in  part, to limited phylogenetic signal. Furthermore, both the  BAPS analysis and the ad hoc Δ&lt;em&gt;K&lt;/em&gt; statistic from  results of the STRUCTURE analysis suggest that population  structure can possibly be captured with fewer genetic  groups. Our findings also suggest that uneven sampling  across taxa may be responsible for the contrasting  inferences of population substructure. Our results  consistently supported two distinct sorediate groups,  ‘&lt;em&gt;L. lupina&lt;/em&gt;’ and &lt;em&gt;L. vulpina&lt;/em&gt;, and subtle  morphological differences support this distinction.  Similarly, the putative apotheciate species ‘&lt;em&gt;L.  lucida&lt;/em&gt;’ was also consistently supported as a distinct  genetic cluster. However, additional studies will be  required to elucidate the relationships of other &lt;em&gt;L.  columbiana&lt;/em&gt; s.l. populations with the two sorediate  genetic clusters.&lt;/p&gt;},
      url = {http://knowledge.uchicago.edu/record/10454},
}